Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches in Bacillus subtilis

Here we use Structure-seq2 to probe the in vivo RNA structurome of B. subtilis grown in the presence and absence of amino acids. We show that the change in global RNA structurome is inversely proportional to the change in abundance upon amino acid starvation and that this trend is pronounced in the stringent response and codY regulons. We also use this data to characterize known and novel RNA switches. Structure-seq2 libraries prepared from RNA extracted from B. subtilis (20 mL cultures) grown to mid-esponential phase in the presence of all amino acids as well as in the absence of all amino acids except glutamine. These were done without and with 50 mM dimethyl sulfate (DMS) added prior to RNA extraction. Three biological replicates were prepared for +/- amino acids and +/- DMS for a total of 12 individual samples. These were labeled with unique Illumina TruSeq barcodes and were sequenced by HiSeq 2500.